The visitors had 15 minutes to respond with an extra man on the field and eventually that difference told as Fernandez fired in an equaliser with three minutes remaining.
The left-back went unchallenged on the edge of the Blues box, saw space to accelerate into the box and fired a shot that proved too hot for Sharman-Lowe to handle.
Despite stoppage-time drama that saw Kovar hobble off injured and Soonsup-Bell fire into the side-netting from a narrow angle, the points were ultimately shared.
The start of our EFL Trophy campaign, away at Exeter City on Tuesday night. Before then, our youth team travel to Tottenham in the Under-18 Premier League on Saturday morning.
Chelsea (3-4-2-1) Teddy Sharman-Lowe; Josh Brooking, Xavier Mbuyamba (c), Bashir Humphreys; Silko Thomas (Dion Rankine h/t), George McEachran, Ben Elliott, George Nunn (Sam McClelland 62); Charlie Webster, Harvey Vale; Jayden Wareham (Jude Soonsup-Bell 62)
Unused subs Bryan Fiabema, Ethan Wady
Scorer Vale (pen) 74
Booked Elliott 35; Webster 90+8
Sent off Brooking 61
Man United Matej Kovar (Dermot Mee 90+2), Charlie Wellens, Alvaro Fernandez, Joseph Olowu, Bjorn Hardley, Martin Svidersky, Shola Shoretire, Charlie Savage (Alejandro Garnacho 87), Charlie McNeil, D’Mani Mellor, Dillon Hoogewerf
Unused subs Marc Jurado, Mateo Mejia
Scorer Fernandez 87
Booked Shoretire 50; Olowu 73
Referee Alan Dale